Actually, in trying to take the photos just now, I can see that it WAS a bug/problem, but it appears to have now been fixed. Now when you use a bill to create an invoice, the markup row does not have a 1 in it, so it isn't miscalculating the quantity and therefore the rate. The invoices had all looked correct when viewing in QB, but incorrect after printing to PDF or sending in a test email. And I had changed nothing on my side so I know I wasn't at fault.
If only they had fixed it BEFORE I had to stay up all night removing the markup lines off 63 very long invoices and hand adjusting each remaining line to be our billing rate not the subcontractor's billing rate.